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<a href="MatrixScorer_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00023"></a>00023 <span class="preprocessor">#ifndef MOLTK_ALIGN_MATRIX_SCORER_H</span>
<a name="l00024"></a>00024 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_ALIGN_MATRIX_SCORER_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span>
<a name="l00026"></a>00026 <span class="preprocessor">#include &quot;<a class="code" href="Aligner_8hpp.html">moltk/Aligner.hpp</a>&quot;</span>
<a name="l00027"></a>00027 <span class="preprocessor">#include &quot;<a class="code" href="units_8hpp.html">moltk/units.hpp</a>&quot;</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &lt;iostream&gt;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00030"></a>00030 
<a name="l00031"></a>00031 <span class="keyword">namespace </span>moltk {
<a name="l00032"></a>00032 
<a name="l00037"></a><a class="code" href="classmoltk_1_1MatrixScorer.html">00037</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a>::Scorer
<a name="l00038"></a>00038 {
<a name="l00039"></a>00039 <span class="keyword">public</span>:
<a name="l00040"></a><a class="code" href="classmoltk_1_1MatrixScorer.html#ab2547e83ca5136945352ab5ef008de4b">00040</a>     <span class="keyword">typedef</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1MatrixScorer.html#ab2547e83ca5136945352ab5ef008de4b">Information</a>;
<a name="l00041"></a>00041 
<a name="l00042"></a>00042     <span class="keyword">explicit</span> <a class="code" href="classmoltk_1_1MatrixScorer.html#a679c59d57d0d690fc2add4204b15deb6">MatrixScorer</a>(<span class="keyword">const</span> std::string&amp; matrix_string);
<a name="l00043"></a>00043     <span class="keyword">explicit</span> <a class="code" href="classmoltk_1_1MatrixScorer.html#a679c59d57d0d690fc2add4204b15deb6">MatrixScorer</a>(std::istream&amp; matrix_stream);
<a name="l00044"></a>00044     std::vector&lt;Aligner::QueryPosition*&gt; <a class="code" href="classmoltk_1_1MatrixScorer.html#a6732a8098d7e4811669934618d5ea1ef">create_query_positions</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00045"></a>00045     std::vector&lt;Aligner::TargetPosition*&gt; <a class="code" href="classmoltk_1_1MatrixScorer.html#adadccdab70f7531e88e619a75dcf58c7">create_target_positions</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00046"></a>00046     std::istream&amp; <a class="code" href="classmoltk_1_1MatrixScorer.html#a24d6950d643f55e6613755404c0c305b">load_stream</a>(std::istream&amp;);
<a name="l00047"></a>00047 
<a name="l00048"></a>00048     <span class="keyword">static</span> <span class="keyword">const</span> <a class="code" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">MatrixScorer</a>&amp; <a class="code" href="classmoltk_1_1MatrixScorer.html#a58a29032f0c197845d1c1cabb4bf2d84">get_blosum62_scorer</a>();
<a name="l00049"></a>00049 
<a name="l00058"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html">00058</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html" title="QueryPosition represents an alignment/sequence column in the second of two sequences being scored by ...">QueryPosition</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a>::<a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html" title="QueryPosition represents an alignment/sequence column in the second of two sequences being scored by ...">QueryPosition</a>
<a name="l00059"></a>00059     {
<a name="l00060"></a>00060     <span class="keyword">public</span>:
<a name="l00061"></a>00061 
<a name="l00062"></a>00062         <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html" title="QueryPosition represents an alignment/sequence column in the second of two sequences being scored by ...">QueryPosition</a>* <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a4db8009ff73af91086b6a00931d43ba6">clone</a>() <span class="keyword">const</span>;
<a name="l00063"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a2dca485364b5b80dbc0a77ffe20af16a">00063</a>         <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a2dca485364b5b80dbc0a77ffe20af16a">get_gap_open_penalty</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a58acc0c7df51b60ffcf81ef1182574df">gap_open_penalty</a>;}
<a name="l00064"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a6dd13920fe7322b872381e6d2f80f3ad">00064</a>         <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a6dd13920fe7322b872381e6d2f80f3ad">get_gap_extension_penalty</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a8e918b0d431d48be6d8f5dcbd9294093">gap_extension_penalty</a>;}
<a name="l00065"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a30c0392023d350e91aadd5a0dcc5f2ca">00065</a>         <span class="keyword">inline</span> <span class="keyword">friend</span> std::ostream&amp; <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a30c0392023d350e91aadd5a0dcc5f2ca">operator&lt;&lt;</a>(std::ostream&amp; os, <span class="keyword">const</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html" title="QueryPosition represents an alignment/sequence column in the second of two sequences being scored by ...">QueryPosition</a>&amp; p)
<a name="l00066"></a>00066         {
<a name="l00067"></a>00067             os &lt;&lt; <span class="stringliteral">&quot;op=&quot;</span> &lt;&lt; p.<a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a2dca485364b5b80dbc0a77ffe20af16a">get_gap_open_penalty</a>();
<a name="l00068"></a>00068             os &lt;&lt; <span class="stringliteral">&quot;, ep=&quot;</span> &lt;&lt; p.<a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a6dd13920fe7322b872381e6d2f80f3ad">get_gap_extension_penalty</a>();
<a name="l00069"></a>00069             <span class="keywordflow">return</span> os;
<a name="l00070"></a>00070         }
<a name="l00071"></a>00071 
<a name="l00072"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a58acc0c7df51b60ffcf81ef1182574df">00072</a>         <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a58acc0c7df51b60ffcf81ef1182574df">gap_open_penalty</a>;
<a name="l00073"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a8e918b0d431d48be6d8f5dcbd9294093">00073</a>         <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a8e918b0d431d48be6d8f5dcbd9294093">gap_extension_penalty</a>;
<a name="l00074"></a>00074         <span class="comment">// cache values for quick score lookup</span>
<a name="l00075"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#aa49abd69aaeaed0b44b30f93f3310fe0">00075</a>         <span class="keyword">typedef</span> std::vector&lt; std::pair&lt;size_t, double&gt; &gt; <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#aa49abd69aaeaed0b44b30f93f3310fe0">QueryWeights</a>;
<a name="l00076"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a79bad8862e87d32644f1b39ad036709d">00076</a>         <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#aa49abd69aaeaed0b44b30f93f3310fe0">QueryWeights</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1QueryPosition.html#a79bad8862e87d32644f1b39ad036709d">residue_type_index_weights</a>;
<a name="l00077"></a>00077     };
<a name="l00078"></a>00078 
<a name="l00079"></a>00079 
<a name="l00084"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html">00084</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html" title="TargetPosition represents an alignment/sequence column in the first of two sequences being scored by ...">TargetPosition</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1Aligner.html" title="The Aligner class creates macromolecule sequence alignments and structure alignments.">Aligner</a>::<a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html" title="TargetPosition represents an alignment/sequence column in the first of two sequences being scored by ...">TargetPosition</a>
<a name="l00085"></a>00085     {
<a name="l00086"></a>00086     <span class="keyword">public</span>:
<a name="l00087"></a>00087 
<a name="l00088"></a>00088         <span class="keyword">virtual</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html" title="TargetPosition represents an alignment/sequence column in the first of two sequences being scored by ...">TargetPosition</a>* <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a283dedf30a28c62172f99c864fdb8dad">clone</a>() <span class="keyword">const</span>;
<a name="l00089"></a>00089         <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">moltk::units::Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#afbdb8ce801576546721721d21c441398">score</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Aligner_1_1QueryPosition.html" title="QueryPosition is an alignment column specialized to efficiently compute an alignment score with a Tar...">Aligner::QueryPosition</a>&amp; rhs) <span class="keyword">const</span>;
<a name="l00090"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a763d419002cf6f6c2fca59d93391e945">00090</a>         <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a763d419002cf6f6c2fca59d93391e945">get_gap_open_penalty</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ae29d8a56f5c10b484d754b79d9d1b8ea">gap_open_penalty</a>;}
<a name="l00091"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a78d5d85f2e0502eee87c28e6b0b969d5">00091</a>         <span class="keyword">virtual</span> <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a78d5d85f2e0502eee87c28e6b0b969d5">get_gap_extension_penalty</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a2bf28e7f278dc41a844eeb17067be4bb">gap_extension_penalty</a>;}
<a name="l00092"></a>00092 
<a name="l00093"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ae29d8a56f5c10b484d754b79d9d1b8ea">00093</a>         <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ae29d8a56f5c10b484d754b79d9d1b8ea">gap_open_penalty</a>;
<a name="l00094"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a2bf28e7f278dc41a844eeb17067be4bb">00094</a>         <a class="code" href="structmoltk_1_1units_1_1Quantity.html" title="Quantity represents a physical value with a unit, such as &quot;5.6 nanometers&quot;.">Information</a> <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#a2bf28e7f278dc41a844eeb17067be4bb">gap_extension_penalty</a>;
<a name="l00095"></a>00095         <span class="comment">// cache values for quick score lookup</span>
<a name="l00096"></a><a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ab3e868c658e21122068e74ec7eaf5048">00096</a>         std::vector&lt;Information&gt; <a class="code" href="classmoltk_1_1MatrixScorer_1_1TargetPosition.html#ab3e868c658e21122068e74ec7eaf5048">scores_by_residue_type_index</a>;
<a name="l00097"></a>00097     };
<a name="l00098"></a>00098 
<a name="l00099"></a>00099 <span class="keyword">protected</span>:
<a name="l00100"></a>00100     <span class="comment">// create_foo_positions is a helper function to reduce redundancy between </span>
<a name="l00101"></a>00101     <span class="comment">// methods create_query_positions() and create_target_positions()</span>
<a name="l00102"></a>00102     <span class="keyword">template</span>&lt;<span class="keyword">class</span> POSB, <span class="keyword">class</span> POS&gt;
<a name="l00103"></a>00103     std::vector&lt;POSB*&gt; <a class="code" href="classmoltk_1_1MatrixScorer.html#aef587746f1419b9b985ee68ff1455f04">create_foo_positions</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1Alignment.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment</a>&amp; alignment) <span class="keyword">const</span>;
<a name="l00104"></a>00104 
<a name="l00105"></a><a class="code" href="classmoltk_1_1MatrixScorer.html#a6a1606c15fde892eedd8bcd83d2b4350">00105</a>     std::vector&lt;int&gt; <a class="code" href="classmoltk_1_1MatrixScorer.html#a6a1606c15fde892eedd8bcd83d2b4350">character_indices</a>; <span class="comment">// maps letters to matrix indices</span>
<a name="l00106"></a><a class="code" href="classmoltk_1_1MatrixScorer.html#ac6fdcde81452d3f0c853b09d0c07f4a9">00106</a>     std::vector&lt; std::vector&lt;Information&gt; &gt; <a class="code" href="classmoltk_1_1MatrixScorer.html#ac6fdcde81452d3f0c853b09d0c07f4a9">matrix</a>;
<a name="l00107"></a>00107 };
<a name="l00108"></a>00108 
<a name="l00109"></a>00109 std::istream&amp; <a class="code" href="namespacemoltk.html#a9d6101e75a7b6c533c256d3bceeae415">operator&gt;&gt;</a>(std::istream&amp;, <a class="code" href="classmoltk_1_1MatrixScorer.html" title="MatrixScorer scores alignments using a residue type matrix such as BLOSUM62 or PAM250.">moltk::MatrixScorer</a>&amp;);
<a name="l00110"></a>00110 
<a name="l00111"></a>00111 } <span class="comment">// namespace moltk</span>
<a name="l00112"></a>00112 
<a name="l00113"></a>00113 <span class="preprocessor">#endif // MOLTK_ALIGN_MATRIX_SCORER_H</span>
<a name="l00114"></a>00114 <span class="preprocessor"></span>
</pre></div></div>
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